Permanent Shadows
by obsessedwithstabler
Summary: A year after John disappears from a crime scene, Sherlock is burning out with nothing to lose. And a man with nothing to lose is a man to fear. Cowritten with Quadrophenia73.
1. Hell

Now presenting our first, full-length Sherlock story, Permanent Shadows! Written with Quadrophenia73, this is an eventual Johnlock story. There is a lot of dark and mature content in this story, so readers beware. Read on and enjoy...

Disclaimer: Not ours!

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_Could be dangerous_.

John groaned, shaking as he lie on the cold ground. Time ceased to hold any kind of meaning for him. He had not seen sunlight in an eternity, and the only human connection he received left him broken and bloody on the floor.

When would this hell end?

* * *

_Sherlock_.

"Sherlock's not coming for you," a voice whispered, driving John mad. "He doesn't care about you. Never did. He's got on with his life, or whatever you would call it."

John turned away from the voice, only to receive a brutal kick to his ribs. They snapped anew but John didn't cry out. He had fought for this long to hold onto what remained of himself. He would keep fighting until he died.

"Oh, tough guy? I can fix that."

The hands grabbed him roughly, digging into his broken ribs and showing no mercy.

No mercy.

More time passed. John's ribs eventually healed, though never properly. His arm was ripped out of the socket and his right leg was broken. Still he held onto hope that one day Sherlock would find him.

* * *

Mrs. Hudson was quiet as she made her way up to Sherlock's flat. A full year had passed since John disappeared from a crime scene and everyone had slowly given up hope. If he was still somehow alive, surely he would have found a way to send word to Sherlock, if no one else.

She let herself into the flat and found it in its usual state of disarray. "Sherlock? Are you home?"

Sherlock stood, staring out the window with an unreadable expression on his face. The condition of both the consulting detective and the flat gave proof that everything was completely wrong. When he heard Mrs. Hudson call his name, he responded quietly, his voice dull. "I'm here."

He could hear the elderly woman's footsteps behind him, but that didn't prompt him to move a muscle. He hadn't received a solid night's sleep in weeks. Without John to sit him down and insist that he eat as a normal person would, he had lost weight until he was much thinner than he already naturally was.

"I brought you dinner, dear heart." She held up a bowl of stew she had made especially for him. "You should eat something."

Sherlock finally turned away from the window. "Eating and digesting slow me down. I have more important things to do." He paced the floor, stopping for a moment in front of the smiley face on the wall, or rather what was left of it among the countless bullet holes he had fired into it with John's gun.

"Sherlock, you're wasting away! What would John say?"

Sherlock was quiet. "He would tell me that my logic is ridiculous, and I would tell him to go away. Then he would insist until I gave in."

"Yes, he would, love." She placed the bowl in his hands. "Please eat a few bites." The look on his face broke her heart all over again. She knew the likelihood of John being dead, but Sherlock refused to come to terms with it. He even kept John's room just the way he'd left it, a shrine for a man who would never come home.

Her words seemed to work. Albeit reluctantly, he sat down in one of the arm chairs and picked up the spoon, eating as he stared emptily into space.

Mrs. Hudson stayed with Sherlock as he ate, wondering the whole time if he would ever be okay again.

* * *

John's entire body ached as he slowly regained consciousness. He pushed himself upright with caution, gasping when his ribs shrieked in protest. "Sherlock," he whimpered before he could stop himself.

There was no reply.

To Be Continued...


	2. Disconnect

Things get rather graphic in this particular chapter. You have been warned.

Disclaimer: Not ours!

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He must have fallen asleep again because the man was back, kicking him awake. John curled into himself and tried to breathe through the constant onslaught of agony.

"Shut up, you fucking maggot," the man hissed, driving his steel toe boot into John's back.

John's entire body seized up and his lip began to bleed as he bit down on it.

The sound the whip made as it cut through the air chilled John to the bone.

* * *

Sherlock rummaged through John's room. Every time he picked something up, he took care to place it exactly as it had been before. He sat down on the bed and stared up at the ceiling. He knew that John was alive. He felt certain that he knew who was behind the entire plot. He had figured out so much.

And it only made him angrier.

He had so much to go on but he was no closer to finding his best friend. A year had passed and he constantly discovered something, but he couldn't get a location no matter how hard he tried.

He knew that Jim Moriarty was to blame. Only the evilly brilliant consulting criminal could come up with a plot challenging enough to put the consulting detective at his wit's end.

Sherlock stood abruptly, cursing under his breath. He cursed Moriarty for dropping off of the face of the earth. He cursed himself for not being able to find John. Angrily he punched the wall, a satisfying pain starting in his knuckles and shooting through his entire arm.

He took several deep breaths and leaned his forehead against the wall, closing his eyes as his shoulders began to shake.

Everyone was beginning to doubt that John was still alive. Their doubt only drove Sherlock's determination harder. He would go nights at a time without sleeping, staying up until the sun rose as he tried desperately to find his friend.

Though there was nobody in the room, he leaned against the wall and started speaking. "John, I know you're out there. Don't give up on me. I'll find you."

* * *

The man finally left the room and John was enveloped by darkness. Tears slowly rolled down his cheeks as he curled up on his side and stifled a sob. Why hadn't Sherlock found him yet? How long could he keep doing this?

A sudden wave of nausea hit him and before he could move, he began to vomit. There was nothing in his stomach after the second heave but his body continued to spasm weakly.

"Poor, poor John," a voice crooned.

John froze. That voice...

"It's okay, honey." There was the distinctive sound of a zipper coming undone and liquid sloshing around in a bottle.

Suddenly John was yanked to his feet by large, rough hands. He cried out and trembled, but otherwise didn't speak.

"Always the tough soldier. That's okay. We'll remedy that." The voice turned cold. "Hold him down."

John was shoved against a wall so brutally that his head bounced off the cinder blocks with an audible thud. Too stunned to cry out, he stood there, dazed and supported by the man who had put him there.

There was the sound of liquid again and John didn't have time to move before it was splashed into his face. A violent scream ripped from his throat as he tried to close his eyes against the chemical agent that burned him. The hands released him and he sank to the floor, crying helplessly.

"Not so tough now, are we?"

A hand grasped his throat and pulled him up again. He fought to breathe but the grip was strong. He wheezed and struggled weakly until the darkness overcame him.

* * *

When he awoke again, John couldn't breathe. He quickly realized something was on top of him, pinning him against the concrete floor.

There was a panting sound in his ear and agony ripped through him as the...the thing on top of him jerked against him.

Burying his face in the concrete, John tried to detach himself. He pictured Sherlock's face, but the more time that passed, the harder it was to remember Sherlock's face. He sobbed at the thought.

Sherlock was slipping away.

The animal on top of him climaxed and rolled away with a satisfied grunt. "Good job, Johnny boy." He slapped John's ass and chuckled as he left the room.

The door slammed shut, the sound reverberating through John's aching head. At least he couldn't see the bastard's face.

He never thought he would be grateful to be blind.

To Be Continued...


	3. Light a Match

Disclaimer: Not ours!

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Chapter Three: Light a Match

Sherlock didn't sleep that night. He was still awake when the sunlight spilled through the window blinds of John's bedroom. He had spent the entire night sitting on the floor with his back to the wall. His hand throbbed, his knuckles split after punching the wall. He flexed his hand and ignored the pain. He stood up and left the bedroom and walked across the living room. He brushed a hand over his violin, the strings squeaking under his fingers, rusty after a year of being left abandoned on the shelf.

He sat down heavily and buried his face in his hands. Exhaustion nagged him but he refused to give in. Sleep wouldn't find John. He knew that if his best friend could see him, he would rush Sherlock into bed and feed him. When he found John, he knew that the former army doctor would be disappointed in him for neglecting himself. Sherlock pushed the thought aside. John's safe return meant more.

He startled when he heard his cell phone beep. He reached into his pocket and retrieved the device. One message from an unknown number. He pushed the button and watched as the text message displayed on his screen. For a moment, his vision blurred. He shook his head, focusing his eyes on the text and reading it, whispering every word out loud. He read it again. And again.

_Missing your pet, are we_? -JM

"Moriarty," he whispered. He pressed the call button, holding his breath. He strained his ears. Somewhere he could hear the criminal's Stayin' Alive ringtone playing. The music sounded alarmingly close. Moriarty was in the flat.

"Hello, dear Sherlock," the consulting criminal greeted as he stepped through the door. "You've really taken the loss of your flatmate quite hard. Just look at you. That's no way for a grown man to care for himself. Lost without your John to take care of you, I suppose?"

Sherlock stood up. "What have you done with him?"

Moriarty smiled. "I'm afraid that I gave him to a new owner long ago. I remain in touch, though. I hear that he mentions your name often. It's really charming how protective he is of you."

Sherlock picked up the gun that sat on the sidetable. "Where is he?" he asked lowly, his voice dropping to a deep whisper. "Don't play games with me. You know where he is."

"Of course I do. Otherwise that would ruin the fun of this scenario!" Moriarty sing-songed, completely unshaken by the presence of Sherlock's weapon pointing inches away from his smug face.

"Tell me where he is," Sherlock growled, his blood boiling with fury.

"I'll get around to that subject eventually."

The only thing that kept Sherlock from pulling the trigger was the sick realization that the man in front of him was the only person who knew where John was. "Take me to him," he demanded. "Now. No games."

"The game's already over. Of course you can see him now." Moriarty started in the direction of the door, Sherlock following him closely.

Sherlock slowly lowered his gun. "You can have me. Let John go. Do anything you want to me. You said you would burn me. Do that. Just don't keep John."

"I already have, darling. I burned you. And your John was just the match I needed to light the fire."

* * *

John whimpered when the door opened again. He had been unable to move for some time now and his captor had been making the most of it.

"Good morning, my little pet. How are we feeling today?"

John remained silent.

"Not feeling sociable? What a pity, and so unromantic!"

The bare floor scraped John's chest as his captor grabbed him and dragged him from his fetal position. He had long since been stripped of any clothes, anything that identified him as human.

When his captor was finished, instead of leaving him there to rot as he usually did, he sat down beside John's head. "Were you so unenthusiastic when Sherlock touched you?" he queried as though he were discussing the weather.

Silence.

"I'm sure he's found a new lover by now. A man like that doesn't stay single for long. Maybe he's married now."

Nothing.

"Probably even has a kid or two. He's moved on with his life and forgotten all about you. The sooner you realize that, the better off you'll be."

He got to his feet and left the room, leaving John in the darkness.

* * *

Sherlock could feel his heart pounding in his ears as he walked down a steep staircase, his legs shaking. He wasn't certain where Moriarty went after leading him into the building, and he didn't care. All that mattered was John.

He reached the bottom of the stairs and stood, his eyes adjusting to the dim lighting. His sight focused on a lump in the floor, near the corner. John.

He started to approach his friend, his feet heavy. "John?" he whispered.

John stirred slightly, grimacing. Was this some new, twisted game? He burrowed further into himself, using his good arm to shield his head.

Sherlock sank to his knees by John's side, reaching out and resting a hand on his friend's arm. "John. It's me."

With violent force, John ripped his arm away and whimpered. Sherlock wasn't there. He wasn't there.

Sherlock immediately pulled his hand away. He had noticed the bruises that covered John's bare body, but he had managed to avoid them when he touched him. The whimper that escaped past John's lips caused Sherlock's anger to escalate. He wanted to protect his friend, but it was evident that the damage had been done. What had the bastards done to him?

The lack of clothing brought a disturbing thought to mind.

Sherlock shook his head, trying to think otherwise. But it all added up. They had raped his best friend. The mere thought made him want to vomit and beat the hell out of whoever had even thought about doing that to John.

"John," he said quietly, keeping his hands at his sides. "You have to listen to me. You're safe. I'm getting you out of here."

This was it. He had finally snapped and lost his mind, or his captor had found a new level of depravity. Either way, he wouldn't give him the satisfaction. With an agonizing amount of effort, he rolled onto his opposite side, away from the hallucination or recording or whatever it was. Sherlock had not found him. Sherlock would not find him. He was getting on with his life and it was for the best.

Sherlock tried again, still taking note of John's injuries. "John, please. Look at me. Open your eyes."

The words hit him like a physical blow. "Why are you doing this?" he managed through swollen lips and a dry tongue.

"Doing what?" That was when he realized it. John didn't believe he was there.

He let out a shaky breath. "I'm really here, John."

"No..." His breathing rattled noisily in his chest.

Sherlock swallowed the lump in his throat. He didn't know where John's captors were or when they would return. "You have to believe me. It's just us, John. You and me. No one else is in this room."

Tears leaked from John's eyes. He wanted so desperately to believe Sherlock was really there, but believing it only to have reality hit him again would kill him. At this point, death would be a welcome reprieve.

Sherlock felt his stomach drop when he saw John's tears. He slipped out of his long coat and draped it over John's shivering frame.

The soft material surrounded John, startling him at first. Then the familiar scent hit his nose. Sherlock. This couldn't be a joke. He recognized the coat by the feel of the fabric. There was no way his captor could have gotten his filthy hands on it. His fingers scrabbled at the soft material. "Sherlock...?"

"Yeah. It's me." Sherlock ran his hand over the coat.

He began to weep openly at the voice. "Sherlock... Oh, God, it's you..."

Sherlock fought to keep his voice strong for John's sake. "I'm here. You'll be alright. You're safe now," he murmured.

Finally John turned back over, his hand extended and reaching. "You...You have to get out of here," he managed, his face flushed. "He's going to...to come back..."

"I'll kill him if he does." Sherlock gently grabbed John's hand. "I'm getting you out of here. Can you stand?"

"Can't...leg's broken..."

Sherlock cringed. "I'll help you. I'm going to have to touch you, alright?" He didn't want to startle his best friend with an unexpected touch and risk upsetting him.

The thought made his stomach revolt, but he trusted Sherlock. He would get him out of this hellhole. "Hurry..." he managed.

"I'll try." Sherlock gently slipped an arm under John's shoulders, avoiding the bruises the best he could. He cringed when he saw the swollen welts down John's back. Carefully, he stood up, supporting all of John's weight.

John couldn't stifle a pained groan. He buried his face in Sherlock's neck and shuddered miserably.

Sherlock was alarmed when he felt how much weight John had lost. He could feel the shorter man's ribs and he wouldn't be surprised if at least some of them were broken. He bent down and hooked his other arm under John's legs, taking care with his injured one, and lifted him into his arms.

Swallowing audibly, John tucked his broken arm between his chest and Sherlock. A horrible part of him still attempted to convince him this was just a fantastic dream, but Sherlock was warm and solid against him. This couldn't be a dream.

Sherlock carefully made his way up the stairs, trying not to jostle John too much, all the while murmuring into his ear in an attempt to soothe him.

John remained silent until he suddenly felt wind on his face and the sun's warm rays. He suddenly tensed. "I have to go back," he choked out.

"No, you don't. I'm taking you to get checked out, and then you're going home. You're not going back there." Sherlock hailed for a cab.

John shuddered and thrashed, but there was no strength in the movements. "No..."

"Shh." Sherlock somehow managed to open the back door of the cab with John still in his arms. He climbed into the backseat. "Get us to the nearest hospital," he ordered the cabby, holding John on his lap.

The cabbie pulled away from the curb, occasionally glancing in the review mirror.

John stiffened when the cab began to move. "Sherlock..."

"Yes?"

John fell silent again. He cautiously moved his head back to Sherlock's neck and coughed.

Sherlock furrowed his brow. John was attempting to turn toward his voice, but his eyes stared straight ahead. "You can't see me..." he mused. They had blinded him. The bastards.

Feeling the coat being wrapped more securely around him, John nodded reluctantly. "How long?" he whispered.

"A year," Sherlock said softly.

"Oh." John's voice was flat. "Seemed a lot longer."

"I know it took a while." Sherlock mentally kicked himself. "But you're out of that place now."

John became quiet, unable to form any more words. His breathing was hoarse and rattled deeply in his chest.

Sherlock adjusted the coat around John again. The cab suddenly hit a sharp bump in the road.

The jarring hit John's body violently. He jerked in agony and pushed his face further into Sherlock's neck, breathing raggedly.

Sherlock gave the cabbie a look that could melt ice. "Be careful," he growled menacingly.

He kept a cold stare directed at the back of the driver's head and gently ran his hand over John's hair.

Finally they arrived at the closest hospital, St. Bartholomew's, and the cabbie stopped the vehicle at the hospital's entrance.

Sherlock pushed the door open and lifted John into his arms again, not bothering to close the cab door or pay the cabbie.

John held tightly to Sherlock, but his strength was waning. His head lolled listlessly against Sherlock's shoulder.

Sherlock walked faster into the emergency room. "Someone get over here!"

Immediately several nurses swarmed them and a gurney was produced. But the moment one hand touched John, he panicked. "Sherlock, don't!"

"John... they need to examine you. I'll go with you. But I need to put you down on the gurney."

"No! He's going to kill me! No needles!" John continued to babble, all the while shaking and gasping for air.

"He's not here. And if he ever shows his face again, I'm going to murder him. I'll protect you. Just listen to me."

A syringe was produced and before Sherlock could protest, the needle was swiftly inserted into John's arm. He howled in vehement protest and tried to hide in Sherlock's coat.

Sherlock clenched his fist angrily. "What the hell did you just give him?"

"Just a mild sedative," the accused nurse replied uneasily. "He'll be fine."

Sure enough, John slowly went lax against Sherlock, but he continued to mutter softly. "Sherlock..."

"I'm here," Sherlock said. "I'm not going anywhere."

"I...hell..." He groaned and moved listlessly, still grasping at Sherlock's coat. "No..."

"You're okay. Just go to sleep." Sherlock ran his hand over John's forehead.

One of the nurses urged Sherlock to place John on the gurney they had provided. He did so reluctantly, then the gurney was rushed around the corner and out of Sherlock's sight.

Sherlock allowed himself to collapse into a chair. He rested his chin on his hands and closed his eyes. A part of him wanted to cry, but he had to stay strong. John needed him.

To Be Continued...


	4. Burn His Heart

Sorry for not updating sooner! I (obsessed) have been planning a trip to Atlanta and this past weekend I attended Walker Stalker Con. For any Dead heads out there, it was a huge convention dedicated to Walking Dead. It was a success, to say the least. Now, as they say, on with the show!

Disclaimer: Not ours!

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Chapter Four: Burn His Heart

A half-hour later, Greg Lestrade barged into the waiting room. His eyes immediately settled on Sherlock. "Is it true?" he demanded. "Is John...?"

Sherlock looked up. "He's alive, if that's what you want to know."

Unable to stand, Lestrade dropped into the chair beside Sherlock and ran his hands through his hair. "A year... He was alive this entire time."

Sherlock didn't say anything. He couldn't bring himself to talk out loud about what had happened to John.

Lestrade started to laugh. He slapped his hands against his legs and leaned forward, blowing out a relieved breath. "Thank God." He had watched Sherlock slowly unravel this past year, to the point of feeling fear every time he was called to a scene because he wondered if this would be the scene Sherlock himself had brought about.

Sherlock still remained silent, unable to understand how or why anyone would want to do such horrible things to John.

Unable to understand why Sherlock wasn't even smiling, Lestrade turned fully to face Sherlock. "He's alive, Sherlock. And you found him, against all odds. It's going to be okay."

"No. No, it's not." Sherlock stood up and took several steps down the hallway John had been taken down.

Hesitating for only a moment, Lestrade launched himself to his feet and went after Sherlock. "What do you mean, it's not? He's alive." A sickening realization hit him suddenly. "How badly was he injured? Was he conscious?"

Sherlock paused. "They really hurt him. He can't see and..." He cut himself off, unsure as to whether or not John would want him to continue.

Lestrade leaned against the closest wall, rubbing his temple slowly. "He'll be okay, Sherlock. He's strong. He'll fight."

"I hope so."

Sherlock leaned his back against the wall opposite Lestrade and let his knees give out. He slunk down the wall until he was sitting on the floor.

Unable to find the right words, Lestrade sat down beside Sherlock, awkwardly patting the younger man's arm.

They sat in silence for a long time, until a doctor in blue scrubs came down the hall. His expression was dark and there was a clipboard in his hand. "Are either of you Sherlock Holmes?"

Sherlock stood up. "That's me. Skip the dull introductions and tell me how he is."

If the doctor was perturbed by Sherlock's bluntness, he didn't show it. "I'm afraid Mr. Watson's condition is very grave. Both his right leg and arm were broken in numerous places, several of his ribs were broken, and he is severely dehydrated and malnourished. He has countless lacerations and superficial wounds, along with poorly healed breaks."

Lestrade got to his feet and stood behind Sherlock, mouth slightly agape as he listened.

"He also has a severe case of pneumonia brought on by a long period in a cold, damp environment. He has a vitamin deficiency, and as well as I can tell he has not been subjected to sunlight for at least eight months."

The doctor looked at the clipboard in his hand. "Then there's the matter of his eyes. There's severe scarring around the eyes themselves, suggesting an attack with some sort of chemical agent. As a result, his vision has been severely impaired. I cannot say with any certainty if he will ever recover his vision."

Sherlock wanted to shout. He wanted to swear. But the logical side of his mind told him that losing his temper wouldn't do anything to help John.

"Finally, we documented severe trauma around his genital area. We performed a rape kit as well as tests for any STDs he may have contracted."

"And?" Sherlock pressed.

"We're awaiting the results of the tests, but he was sexually assaulted numerous times over the last nine months."

Sherlock felt nauseous. He opened his mouth but found it difficult to form words.

"He's currently in the Intensive Care Unit, under heavy sedation." For a moment, the doctor's eyes turned sympathetic. "I suggest you both go home. There's nothing more you can do for him."

Sherlock didn't move. "I'm not going anywhere."

"You won't be able to see him until tomorrow, at the earliest."

"Don't care."

Lestrade stepped in front of Sherlock. "The man in your care is Dr. John Watson. He has been missing, presumed dead, for a year, and this man was able to find him when no one else could. He's Dr. Watson's closest friend and only family, so don't expect him to leave this hospital until he's been allowed to see Dr. Watson."

"I understand that, but my patient comes first. He'll be allowed to have one visitor tomorrow evening if his condition allows it, and no earlier."

"I'm staying here," Sherlock said firmly.

"Very well. A nurse will be out with an update in a couple of hours."

Sherlock, though only slightly satisfied, sat down in a vacant chair. A few hours was far too long to wait, but he had established that he would be staying.

Lestrade followed Sherlock but didn't sit. "I should start making calls. Is there anyone you would like me to contact first?"

Sherlock thought for a moment. "I have a call to make on my own."

"Very well. I'm going to step outside and make those calls." He turned around and left Sherlock alone in the waiting lounge.

It wasn't much later when Mycroft arrived at the hospital. He found his younger brother in the waiting room. "I arranged it. They'll move him into the best room they have."

"Good." Sherlock turned around to face him. Mycroft had watched as Sherlock slowly tore himself to pieces throughout the year that had passed. He kept Sherlock under his close but discreet watch almost constantly. Now Sherlock looked on the verge of a total breakdown. "I have a feeling there's something I'm unaware of. Otherwise you wouldn't have called me to show up in person."

It took Sherlock a few tries to find his voice, and when he did it was hoarse. "They blinded him with chemicals. The doctor thinks it's permanent." He paused for a moment, trying to control the trembling of his voice. "They raped him," he whispered. His knees stopped working and he fell into a chair and buried his face into his hands.

Mycroft sat next to him. "I told you that caring is not an advantage. But I was wrong. All you can do now is care for John."

"But I could be doing something else instead of expressing feelings," Sherlock argued. "I could be finding the bastards and killing them in cold blood!"

"I'll see to it that they're found."

"Promise me," Sherlock demanded, trying to keep tears of anger at bay.

"I promise." Mycroft stood to leave. Before he could walk away, Sherlock stood and grabbed his arm. "Yes?"

"When they are found, make sure they're killed. Brutally. I'll do it myself if no one else will. When John's awake, I'll walk out this door and tear them all apart."

Mycroft didn't doubt the threat in the slightest. He had never seen his little brother in such a mess of anger and sadness at the same time. "I'll make sure they have it hard."

Sherlock sighed in relief and managed a nod. "Good." He started to walk down the hall. He stopped and hesitated before calling over his shoulder, "Thank you, Mycroft."

It wasn't until Sherlock had disappeared around the corner that Mycroft finally responded.

"You're welcome, brother."

To Be Continued...


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